Re^6: Listing of files using glob

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Re^7: Listing of files using glob by MidLifeXis (Monsignor) on Jan 05, 2012 at 13:26 UTC
> Any errors or wrong approach?? Yep. You never chomp the data read from the filehandle `FILE`. Since you are building the file name directly from the line read, it most likely contains a newline. If you print your value for `$line` with a delimiter surrounding it (`print "'$line'\n";`) you will see what I mean. See chomp (as has been previously mentioned) for a solution. Update: Since the OP is using $& to populate the hash, and the processing loop uses the keys of the hash as the name of the file, the newline from the file should not be included in the hash key. Nice catch choroba I wonder what the line endings are in the data file. Is it possible that the file is in DOS line ending format? In which case, the chomp (and `$&`?) would not do the right thing. --MidLifeXis	[reply] [d/l] [select]
Re^8: Listing of files using glob by choroba (Cardinal) on Jan 05, 2012 at 14:03 UTC
It's a bit more complicated. The OP uses $& as the hash key after matching />.*/, which removes the newline (as . does not match a newline), but it can overwrite a previous hash value if the line does not match, which we cannot tell without seeing the input data.	[reply]
Re^9: Listing of files using glob by MidLifeXis (Monsignor) on Jan 05, 2012 at 14:12 UTC
Aaah, quite right. I am curious about the line endingness of FILE then (in which case, chomp would not do the right thing either :-/ ) --MidLifeXis	[reply]
Re^9: Listing of files using glob by AG87 (Acolyte) on Jan 06, 2012 at 05:16 UTC
The input data is like `>1elwA AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF >1flwA GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ >1ghwA KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO` [download] Where >1elwA, >1flwA, >1ghwA should be the keys of the hashes and the respective data should be the value of the hash. The code/sub for storing in the file is `#!/usr/bin/perl my %seqInfo = (); open(FILE, 'test.fasta'); { while(<FILE>) { my $line = $_; if ($line =~ />.*/) { #print "$&\n"; } else { #print "$line\n"; } $seqInfo{$&} = $line; print "$& => $line\n"; } }` [download] and the output is `=> >1elwA => AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF => >1flwA => GGGGGGGGGGHHHHHHHHHHHHIIIIIIIIIIIIIIJJJJJJJJJJ => >1ghwA => KKKKKKKKKKLLLLLLLLLLMMMMMMMMMMNNNNNNNNNNOOOOO` [download] However according to my understanding the output should be like `>1elwA => AAAAAASSSSSSSSSSSSSSDDDDDDDDDDDFFFFFFFFFF` [download] Maybe the file is not properly stored as keys and values :( :(	[reply] [d/l] [select]
Re^10: Listing of files using glob by AG87 (Acolyte) on Jan 06, 2012 at 08:54 UTC
Re^7: Listing of files using glob by choroba (Cardinal) on Jan 05, 2012 at 13:22 UTC
Can you show the input, too?	[reply]